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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND RNA BINDING DOMAIN IN RNA-BINDING PROTEIN 30
 
Authors :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Mar 06  (Deposition) - 15 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Second Rna Binding Domain In Rna-Binding Protein 30
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN 30
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP051017-04
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GeneRBM30
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRNA-BINDING MOTIF PROTEIN 30, RNA-BINDING MOTIF PROTEIN 4B

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DGT)

(-) Sites  (0, 0)

(no "Site" information available for 2DGT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DGT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DGT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064766E93VRBM4B_HUMANPolymorphism  ---AE93V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM4B_HUMAN2-72
78-148
  1-
A:78-148

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003100461aENSE00002166677chr11:66445392-66445235158RBM4B_HUMAN-00--
1.2bENST000003100462bENSE00001755807chr11:66444562-66444139424RBM4B_HUMAN1-1381381A:68-13871
1.4bENST000003100464bENSE00001188175chr11:66436762-66436086677RBM4B_HUMAN138-3592221A:138-159 (gaps)24
1.6dENST000003100466dENSE00001188165chr11:66433049-66432469581RBM4B_HUMAN-00--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:92
 aligned with RBM4B_HUMAN | Q9BQ04 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:94
                                    77        87        97       107       117       127       137       147       157    
          RBM4B_HUMAN    68 EASKNKSKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPGMGDQSG 161
               SCOP domains d2dgta_ A: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee......hhhhhhhhhhh.....eeee...eeeeee.hhhhhhhhhhhhh.eee..eeeeeee.........--..... Sec.struct. author
                 SAPs(SNPs) -------------------------V-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  -----RRM  PDB: A:78-148 UniProt: 78-148                                     ------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:68-138 UniProt: 1-138 [INCOMPLETE]                   ----------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.4b [INCOMPLETE]   Transcript 1 (2)
                 2dgt A  68 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAS--GPSSG 159
                                    77        87        97       107       117       127       137       147      |155    
                                                                                                                154  |    
                                                                                                                   155    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DGT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DGT)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (RBM4B_HUMAN | Q9BQ04)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0043153    entrainment of circadian clock by photoperiod    The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        RBM4B_HUMAN | Q9BQ042dnq

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